2P42
Complex of a camelid single-domain vhh antibody fragment with RNASE A at 1.8A resolution: SE3-mono-2 crystal form with three se-met sites (M34, M51, M83) in vhh scaffold
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION | 7.5 | 295 | HAMPTON RESEARCH INDEX SCREEN, SOLUTION #85: MGCL2, PEG3350, HEPES BUFFER, PH 7.5, VAPOR DIFFUSION, temperature 295K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.29 | 46.37 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 69.545 | α = 90 |
| b = 55.002 | β = 100.21 |
| c = 65.705 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 1 21 1 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 210 | MIRROR | 2004-04-01 | M | MAD | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 17-ID | 0.97955, 0.97936 | APS | 17-ID |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | ||||||||
| 1 | 1.8 | 20 | 98.1 | 0.095 | 1.8 | 44260 | 44260 | ||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
| X-RAY DIFFRACTION | MAD | THROUGHOUT | 1.8 | 20 | 44260 | 42032 | 2228 | 98.07 | 0.17275 | 0.17275 | 0.17053 | 0.21544 | RANDOM | 17.233 | |||||
| Temperature Factor Modeling | ||||||
|---|---|---|---|---|---|---|
| Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
| -0.93 | 1.22 | -0.23 | 1.59 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 34.355 |
| r_dihedral_angle_3_deg | 13.808 |
| r_dihedral_angle_4_deg | 13.222 |
| r_dihedral_angle_1_deg | 6.489 |
| r_scangle_it | 3.467 |
| r_scbond_it | 2.511 |
| r_mcangle_it | 1.531 |
| r_mcbond_it | 1.256 |
| r_angle_refined_deg | 1.131 |
| r_angle_other_deg | 0.702 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 3722 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 473 |
| Heterogen Atoms | 1 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| HKL-3000 | data collection |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
| SOLVE | phasing |
